Site-specific binding of proteins to DNA plays an important role in cell development, cell signaling, the cell cycle, and diseases such as cancer. There are two overarching goals to this proposal: (1) to develop a means for the identification of proteins bound to specific DNA sequences, and (2) to develop a better method for the identification of immunoprecipitation (IP) functional affinity reagents against DNA-bound proteins found on a complex antigen source. We propose to apply the proof-of-principle using the interaction of transcription factors (TFs) and their specific DNA binding sites as a model. TFs are one major example of such DNA-binding proteins. Once bound to their binding site(s), TF proteins can regulate the transcription of genes, thereby making individual genes either more or less active. Although this is a proposal to develop a better means toward obtaining functional affinity reagents against proteins when they are bound to DNA, the method itself can be applied to other uses.